Re: [base] pb with jsvc/Tomcat
Sorry, I just sent an empty message to the list, apologies...(keyboard shortcuts can be a bad thing). Are you trying to run Tomcat as a service? You shouldn't really have any problems of this sort if you just go for the non-service binary version of Tomcat (http://mirror.public-internet.co.uk/apache/tomcat/tomcat-5/v5.5.20/bin/ apache-tomcat-5.5.20.zip for Windows or http://mirror.public-internet.co.uk/apache/tomcat/tomcat-5/v5.5.20/bin/a pache-tomcat-5.5.20.tar.gz ). You should be able to run this as any user, just by executing the startup.bat or startup.sh scripts in the bin directory. I never had to compile any additional components under this setup, it works straight out of the box for any user on either platform. Cheers Micha == Dr Micha M Bayer Bioinformatics Specialist Genetics Programme The Scottish Crop Research Institute Invergowrie Dundee DD2 5DA Scotland, UK Telephone +44(0)1382 562731 ext. 2309 Fax +44(0)1382 562426 http://www.scri.sari.ac.uk/MichaBayer.htm = -Original Message- From: [EMAIL PROTECTED] [mailto:basedb-users- [EMAIL PROTECTED] On Behalf Of Emmanuel Courcelle Sent: 28 November 2006 10:15 To: BASE ML Subject: [base] pb with jsvc/Tomcat Hello everybody My question is not completely BASE-related, but may be someone around here knows the solution... I would like not to run Tomcat as root user, just for security reasons: it is well known that a web-server like apache should never be started as root, I don't see any reason why it should be different with tomcat. So, as far as I have understood anything, the only way to start Tomcat as no-root is compiling and using the jsvc binary, which is given with tomcat. All is OK, except for one (important, however...) thing: when I try to start some plot tool, tomcat crashes with the message: X11 connection rejected because of wrong authentication. Any idea ? -- Emmanuel COURCELLE[EMAIL PROTECTED] L.I.P.M. (UMR CNRS-INRA 2594/441) tel (33) 5-61-28-54-50 B.P.52627 - 31326 CASTANET TOLOSAN Cedex - FRANCE -- - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDE V ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ DISCLAIMER: This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. It may not be disclosed or used by any other than that addressee. If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify [EMAIL PROTECTED] quoting the name of the sender and delete the email from your system. Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any). - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] long term future and support for BASE2
Hi, This is a non-technical question, for a change. We are about to make a fairly long-term commitment to BASE as our microarray platform and were wondering what the future looks like for BASE, in terms of support and funding (we're talking the next few years rather than months here). This is obviously an issue with all open source projects, and I 'm sure BASE is no exception. I guess many other users may be in the same boat -- no-one wants the support for their system to suddenly dry up, and then to have to migrate their data to something else. It would be good if someone could shed some light on this. Thanks Micha == Dr Micha M Bayer Bioinformatics Specialist Genetics Programme The Scottish Crop Research Institute Invergowrie Dundee DD2 5DA Scotland, UK Telephone +44(0)1382 562731 ext. 2309 Fax +44(0)1382 562426 http://www.scri.sari.ac.uk/MichaBayer.htm = _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ DISCLAIMER: This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. It may not be disclosed or used by any other than that addressee. If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify [EMAIL PROTECTED] quoting the name of the sender and delete the email from your system. Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any). - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] long term future and support for BASE2
Hi, This is a fair question. We are four people involved in the BASE project as programmer in more or lesser degree (Nicklas and Martin are full time employed to work on BASE). We also have a close collaboration with the Oncology Department here in Lund and they also put effort in BASE (1 and 2) progress. The software part of BASE crew is funded until the end of 2009. BASE is an essential part of the core service at the microarray facility here at Lund University so we expect to be supporting BASE at least during this time. What happens beyond 2010 depends on so many things... So, jump on to BASE and help us make the software better. Cheers, Jari Micha Bayer wrote: Hi, This is a non-technical question, for a change. We are about to make a fairly long-term commitment to BASE as our microarray platform and were wondering what the future looks like for BASE, in terms of support and funding (we're talking the next few years rather than months here). This is obviously an issue with all open source projects, and I 'm sure BASE is no exception. I guess many other users may be in the same boat -- no-one wants the support for their system to suddenly dry up, and then to have to migrate their data to something else. It would be good if someone could shed some light on this. Thanks Micha == Dr Micha M Bayer Bioinformatics Specialist Genetics Programme The Scottish Crop Research Institute Invergowrie Dundee DD2 5DA Scotland, UK Telephone +44(0)1382 562731 ext. 2309 Fax +44(0)1382 562426 http://www.scri.sari.ac.uk/MichaBayer.htm = _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ DISCLAIMER: This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. It may not be disclosed or used by any other than that addressee. If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify [EMAIL PROTECTED] quoting the name of the sender and delete the email from your system. Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any). - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED] -- Jari Häkkinen, PhD Complex Systems Divisionmailto:[EMAIL PROTECTED] Department of Theoretical Physics phone: +46 (0)46 2229347 Lund University fax: +46 (0)46 2229686 Sölvegatan 14a, SE-223 62 Lund, Sweden http://www.thep.lu.se - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] Imagene data import
We have been using base 1.2 for a year now. The batch importer we had created for base 1 is useless for base2. Therefore we are moving to using the UI to import each chip. We are using the ImaGene quantitation software and which seems to be supported in base2. But I cannot figure out now to import raw data. Is there no way to merge files from different channels? Thank you, Anup Parikh - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
[base] Offline files
Hi everybody, I have two questions: 1) is there a way to download images or raw data files in batches? 2) while I was trying that (to download more than one file at once), in the 'Files and Directories' tree, I accidentally moved Offline some files, and now I don't seem able to download them anymore. Is there a way to restore them in the Primary position? Thanks in advance Giovanni - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Offline files
Giovanni Coppola wrote: Hi everybody, I have two questions: 1) is there a way to download images or raw data files in batches? No. 2) while I was trying that (to download more than one file at once), in the 'Files and Directories' tree, I accidentally moved Offline some files, and now I don't seem able to download them anymore. Is there a way to restore them in the Primary position? They have been deleted from the server. You have to upload them again. /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
Re: [base] Imagene data import
Anup Parikh wrote: We have been using base 1.2 for a year now. The batch importer we had created for base 1 is useless for base2. Therefore we are moving to using the UI to import each chip. We are using the ImaGene quantitation software and which seems to be supported in base2. But I cannot figure out now to import raw data. Is there no way to merge files from different channels? The current importers can only import data if everything is in one file. There are two options: 1. Merge the files before uploading them to BASE 2. Create an import plugin that can import Imagene files Anyone who volunteer for this? /Nicklas - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to [EMAIL PROTECTED]
